annotateTiles {MOCHA}

annotateTiles

Description

annotateTiles annotates a set of sample-tile matrices given with gene annotations. Details on TxDb and Org annotation packages and available annotations can be found at Bioconductor: https://bioconductor.org/packages/3.15/data/annotation/

Usage

annotateTiles(Obj, TxDb = NULL, Org = NULL, promoterRegion = c(2000, 100))

Arguments

Obj

A RangedSummarizedExperiment generated from getSampleTileMatrix, containing TxDb and Org in the metadata. This may also be a GRanges object.

TxDb

The annotation package for TxDb object for your genome. Optional, only required if Obj is a GRanges.

Org

The genome-wide annotation for your organism. Optional, only required if Obj is a GRanges.

promoterRegion

Optional list containing the window size in basepairs defining the promoter region. The format is (upstream, downstream). Default is (2000, 100).

Value

Obj, the input data structure with added gene annotations (whether GRanges or SampleTileObj)

Examples

## Not run: 
library(TxDb.Hsapiens.UCSC.hg38.refGene)
library(org.Hs.eg.db)
SampleTileMatricesAnnotated <- MOCHA::annotateTiles(
  SampleTileMatrices,
  TxDb = TxDb.Hsapiens.UCSC.hg38.refGene,
  Org = org.Hs.eg.db
)

## End(Not run)